def test_get_pixels_type():
image_processor = image_processor_impl()
conn_settings = CONFIG['omero_conn']
broker = OMERODataBroker(conn_settings,
image_processor=image_processor_impl())
broker.open_omero_session()
query_service = broker.SESSION.getQueryService()
convert_to_uint16 = True
dir_path = os.path.join(
PROJECT_DIR, "..",
"Morph_Batgirl_OldCamera_Htb2_Myo1_Hog1_Lte1_Vph1_00")
common_path = os.path.commonprefix(dir_path)
cube_dirs = glob.glob(''.join([common_path, 'pos???']))
for path in cube_dirs:
if os.path.isdir(path) == True:
for f in os.listdir(path):
fullpath = os.path.join(path, f)
plane = script_utils.getPlaneFromImage(fullpath)
pixelsType = image_processor.get_pixels_type(
plane, query_service, convert_to_uint16)
def main():
CONFIG_FILE = os.path.join(PROJECT_DIR, 'config_test.yml')
CONFIG = {}
with open(CONFIG_FILE, 'r') as cfg:
CONFIG = yaml.load(cfg, Loader=yaml.FullLoader)
conn_settings = CONFIG['omero_conn']
broker = OMERODataBroker(conn_settings)
cache_manager = OmeroCacheManager()
# broker.open_omero_session()
dir_path = os.path.join(
PROJECT_DIR, "tests", "test_data",
"Morph_Batgirl_OldCamera_Htb2_Myo1_Hog1_Lte1_Vph1_00")
# cache_manager.create_db_info(broker)
# cache_manager.save_matlab_object()
cache_manager.save_db_data(broker)
cache_manager.load_matlab_object()
# upload_metadata(broker, dir_path)
broker.close_omero_session()
def omero_data_broker(self):
CONFIG = {}
CONFIG['username'] = '******'
CONFIG['password'] = '******'
CONFIG['server'] = 'localhost'
CONFIG['port'] = 4064
'''Returns a default OMERO data broker for localhost'''
return OMERODataBroker(CONFIG)
def omero_session(self, omero_data_broker):
CONFIG = {}
CONFIG['username'] = '******'
CONFIG['password'] = '******'
CONFIG['server'] = 'localhost'
CONFIG['port'] = 4064
broker = OMERODataBroker(CONFIG)
omero_data_broker.open_omero_session()
print("teardown smtp")
def search_by_type_field(self, type, field, value, case_sensitive=False):
broker = OMERODataBroker(username=self.USERNAME, password=self.PASSWORD, server=self.SERVER, port=self.PORT,
image_processor=DefaultImageProcessor())
broker.open_omero_session()
objects = broker.find_objects_by_type_field_value(type, field, value, case_sensitive)
broker.close_omero_session()
return objects
def search_by_query(self, query, params):
broker = OMERODataBroker(username=self.USERNAME, password=self.PASSWORD, server=self.SERVER, port=self.PORT,
image_processor=DefaultImageProcessor())
broker.open_omero_session()
objects = broker.find_objects_by_query(query, params)
broker.close_omero_session()
return objects
def launch_upload(self, dataset_name, data_path, hypercube=False,
parser_class=MetadataAggregator, image_processor_impl=DefaultImageProcessor,
include_provenance_kvps=True, ignore_metadata=False):
# override `parser_class` for custom metadata extractor implementations
if parser_class is None:
from omero_metadata_parser.aggregate_metadata import MetadataAggregator as parser_class
# override `image_processor_impl` for custom image processing implementations
if image_processor_impl is None:
from omero_data_transfer.default_image_processor import DefaultImageProcessor as image_processor_impl
# conn_settings = config['omero_conn']
broker = OMERODataBroker(username=self.USERNAME, password=self.PASSWORD, server=self.SERVER, port=self.PORT,
image_processor=image_processor_impl())
# broker.open_omero_session()
data_transfer_manager = DataTransferManager(parser_class=parser_class)
results = data_transfer_manager.upload_data_dir(broker, dataset_name, data_path, hypercube=hypercube,
include_provenance_kvps=include_provenance_kvps,
ignore_metadata=ignore_metadata)
# upload_metadata(broker, dir_path)
# broker.close_omero_session()
# Print results
image_id_list = results['image_id_list']
output_str = 'Number of images uploaded'
if hypercube is True:
output_str = 'Number of hypercubes uploaded'
if image_id_list is not None:
print(': '.join([output_str, str(len(image_id_list))]))
dataset_id = results['dataset_id']
if dataset_id is not None:
print(': '.join(['Uploaded Dataset ID', str(dataset_id)]))
dataset_param = '-'.join(['?show=dataset', str(dataset_id)])
dataset_url = '/'.join(['http:/', self.SERVER, 'webclient', dataset_param])
print(': '.join(['Uploaded Dataset URL', dataset_url]))
else:
print('No dataset ID generated - failed to upload dataset')
return dataset_id
def main():
PROJECT_DIR = os.path.join(os.path.dirname(os.path.realpath(__file__)), "..", "..")
CONFIG_FILE = os.path.join(PROJECT_DIR, 'config_test.yml')
CONFIG = {}
with open(CONFIG_FILE, 'r') as cfg:
CONFIG = yaml.load(cfg, Loader=yaml.FullLoader)
conn_settings = CONFIG['omero_conn']
broker = OMERODataBroker(CONFIG,
image_processor=image_processor_impl())
broker.open_omero_session()
# dir_path = os.path.join("","/var","data_dir")
dir_path = os.path.join(PROJECT_DIR,"..","Morph_Batgirl_OldCamera_Htb2_Myo1_Hog1_Lte1_Vph1_00")
data_transfer_manager = DataTransferManager()
data_transfer_manager.upload_data_dir(broker, "test_dataset", dir_path, hypercube=False)
# upload_metadata(broker, dir_path)
broker.close_omero_session()
def searcher(self):
broker = OMERODataBroker(username=self.USERNAME, password=self.PASSWORD, server=self.SERVER, port=self.PORT,
image_processor=DefaultImageProcessor())
broker.open_omero_session()
return broker